Meeting Notes
- Date: 2025-07-01
- Time: 09:00 (PT)
- Location: Teams Meeting
- Presentations: @severine2305 @Dedalus9 @jeromelecoq
Agenda
- Severine will present Neuropixel targetting strategy.
- Nicholas will present statistical power analysis.
- Jerome will introduce finalized stimulus design of next experiment.
Meeting Recording
Meeting Notes
Neuropixel Experiments
Neuropixel Targeting Strategy: Severine presented the neuropixel targeting strategy, explaining the process of creating a shield implant, simulating probe insertions, and testing on pilot mice before finalizing the design for production mice.
Strategy Overview: Severine explained the neuropixel targeting strategy, which involves creating a shield implant, importing it into the Pinpoint software, simulating probe insertions, and testing on pilot mice. The process is iterative, with adjustments made based on feedback from the pilot tests before finalizing the design for production mice.
Shield Implant: The shield implant covers a whole hemisphere of the brain and is made of 3D-printed resin. It allows for precise targeting and reduces the need for multiple craniotomies, minimizing damage to the brain.
Simulation Process: Severine described the simulation process in the Pinpoint software, where the implant is imported, and probe insertions are simulated to ensure they cross the targeted brain areas. Adjustments are made based on the simulation results to optimize the targeting strategy.
Pilot Testing: The strategy includes testing the shield implant on pilot mice to gather feedback and make necessary adjustments to hit thedesired targets. This iterative process ensures the final design is effective for production mice.
Shield Implant Design: Severine described the s implant design, which covers a whole hemisphere of the brain and is made of 3D-printed resin. The implant allows for precise targeting and reduces the need for multiple craniotomies.
Implant Coverage: The shield implant covers an entire hemisphere of the brain, providing extensive access for probe insertions while minimizing the need for multiple craniotomies.
Material and Construction: The implant is made of 3D-printed resin, which is durable and suitable for precise targeting. Severine highlighted the use of CAD software to design the implant and ensure accurate placement of probe holes.
Reduction of Craniotomies: Severine emphasized that the shield implant reduces the need for multiple craniotomies, which can cause significant damage to the brain. By using a single large craniotomy, the implant minimizes trauma and allows for better recovery of the mice.
Pinpoint Software: Severine demonstrated the use of Pinpoint software for importing the shield implant and simulating probe insertions to target specific brain areas.
Software Demonstration: Severine demonstrated how the Pinpoint software is used to import the shield implant and simulate probe insertions. The software allows for precise targeting by visualizing the implant on a CCF brain model and ensuring the probes cross the desired brain areas.
Simulation Accuracy: The Pinpoint software provides a detailed simulation of probe insertions, helping to identify and correct any issues before actual surgery. This ensures that the probes will accurately target the intended brain areas during the experiment.
Adjustments and Iterations: Severine explained that the simulation process is iterative, with adjustments made based on the simulation results. This helps to refine the targeting strategy and improve the accuracy of the probe insertions.
Probe Selection: Severine discussed the selection of probes for targeting specific brain areas, comparing the effectiveness of probe A and probe F for targeting ACA, MoS, IL, PL, and other areas.
Probe Comparison: Severine compared the effectiveness of probe A and probe F for targeting specific brain areas such as ACA, MoS, IL, PL, and others. She highlighted the differences in their angles and how they affect the targeting accuracy.
Simulation Results: Severine presented the simulation results for both probes, showing how each probe crosses the targeted areas. She noted that probe F provided better coverage for certain areas due to its angle.
Final Decision: Based on the simulation results, Severine suggested using probe F for the frontal hole as it provided better coverage for the targeted areas. The decision was made to proceed with probe F for the experiments.
Coordinates and Targeting: Severine and Jordan discussed the coordinates for targeting ACA and other areas, considering the differences between the coordinates used in the papers and the ones used in their simulations.
Coordinate Comparison: Severine and Jordan compared the coordinates used in their simulations with those from the papers. They discussed the differences and how they might affect the targeting accuracy.
Adjustments: Severine suggested adjusting the coordinates to better match the ones used in the papers, which might improve the targeting accuracy for ACA and other areas.
Consensus: After discussing the differences and potential adjustments, Severine and Jordan reached a consensus on the coordinates to use for the experiments. They agreed to make slight adjustments to improve targeting accuracy.
Four Shank Probes: Alexander suggested using four shank probes in V1 to take advantage of the columnar organization and improve current source density analysis. Severine expressed concerns about the difficulty of annotating the probes.
Proposal: Alexander proposed using four shank probes in V1 to leverage the columnar organization and enhance current source density analysis. He explained the potential benefits of this approach.
Concerns: Severine raised concerns about the difficulty of annotating the four shank probes, as it would require multiple insertions and could complicate the analysis.
Discussion: The team discussed the feasibility of using four shank probes, considering the potential benefits and challenges. They explored ways to address the annotation difficulties and improve the overall analysis.
SLAP2 Experiment Analysis
Statistical Power Analysis: Nicholas presented his ongoing work on statistical power analysis, focusing on the reliability of orientation tuning vectors and the impact of the oddball block on synaptic responses.
Analysis Overview: Nicholas presented his work on statistical power analysis, focusing on the reliability of orientation tuning vectors and the impact of the oddball block on synaptic responses. He explained the methodology and preliminary findings.
Reliability Metrics: Nicholas discussed the metrics used to evaluate the reliability of orientation tuning vectors, including the Pearson correlation and the Raleigh vector strength. He explained how these metrics help assess the consistency of tuning across blocks.
Preliminary Findings: Nicholas shared preliminary findings indicating that orientation tuning vectors are more reliable in the post block compared to the pre block. He suggested that the oddball block might enhance tuning reliability.
Orientation Tuning Reliability: Nicholas's analysis suggested that orientation tuning vectors are more reliable in the post block compared to the pre block, indicating stronger tuning after the presentation of the oddball block.
Reliability Increase: Nicholas's analysis showed that orientation tuning vectors are more reliable in the post block, suggesting that the oddball block enhances tuning reliability. He presented data supporting this finding.
Statistical Tests: Nicholas used various statistical tests to assess the reliability of orientation tuning vectors, including ANOVA and nonparametric tests. He explained the results and their implications for understanding tuning reliability.
Implications: The findings suggest that the oddball block has a significant impact on tuning reliability, which could have implications for future experiments and analyses. Nicholas highlighted the importance of considering these effects in experimental design.
Administration
Future Experiments: Jerome proposed running experiments with the finalized stimulus design this week, incorporating Lucas's suggestion to extend the orientation blocks to account for adaptation effects.
Upcoming Meetings: Jerome announced that he will be away for the second half of July and suggested taking a break from meetings during that time to consolidate analysis and refine the experimental design.